docs: Update citation to JOSS article (#2740)

- Replace the BibTeX citation with a Citation File Format (CFF) that references
our new paper in the Journal of Open Source Software.
- Update README and docs to display the JOSS DOI badge and provide proper citation instructions for "Mesa 3: Agent-based modeling with Python in 2025".

Author: EwoutH

CITATION.bib

@@ -0,0 +1,62 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Hoeven
+  given-names: Ewout
+  name-particle: ter
+  orcid: "https://orcid.org/0009-0002-0805-3425"
+- family-names: Kwakkel
+  given-names: Jan
+  orcid: "https://orcid.org/0000-0001-9447-2954"
+- family-names: Hess
+  given-names: Vincent
+  orcid: "https://orcid.org/0000-0002-9242-8500"
+- family-names: Pike
+  given-names: Thomas
+  orcid: "https://orcid.org/0000-0003-1576-0283"
+- family-names: Wang
+  given-names: Boyu
+  orcid: "https://orcid.org/0000-0001-9879-2138"
+- family-names: rht
+  orcid: "https://orcid.org/0009-0002-6902-111X"
+- family-names: Kazil
+  given-names: Jackie
+  orcid: "https://orcid.org/0000-0002-8300-7384"
+doi: 10.5281/zenodo.15090710
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Hoeven
+    given-names: Ewout
+    name-particle: ter
+    orcid: "https://orcid.org/0009-0002-0805-3425"
+  - family-names: Kwakkel
+    given-names: Jan
+    orcid: "https://orcid.org/0000-0001-9447-2954"
+  - family-names: Hess
+    given-names: Vincent
+    orcid: "https://orcid.org/0000-0002-9242-8500"
+  - family-names: Pike
+    given-names: Thomas
+    orcid: "https://orcid.org/0000-0003-1576-0283"
+  - family-names: Wang
+    given-names: Boyu
+    orcid: "https://orcid.org/0000-0001-9879-2138"
+  - family-names: rht
+    orcid: "https://orcid.org/0009-0002-6902-111X"
+  - family-names: Kazil
+    given-names: Jackie
+    orcid: "https://orcid.org/0000-0002-8300-7384"
+  date-published: 2025-03-28
+  doi: 10.21105/joss.07668
+  issn: 2475-9066
+  issue: 107
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 7668
+  title: "Mesa 3: Agent-based modeling with Python in 2025"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.07668"
+  volume: 10
+title: "Mesa 3: Agent-based modeling with Python in 2025"

CITATION.cff

@@ -1,11 +1,12 @@
 # Mesa: Agent-based modeling in Python
 
-| | |
-| --- | --- |
-| CI/CD | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
+|         | |
+|---------| --- |
+| CI/CD   | [![GitHub Actions build status](https://github.com/projectmesa/mesa/workflows/build/badge.svg)](https://github.com/projectmesa/mesa/actions) [![Coverage status](https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa) |
 | Package | [![PyPI - Version](https://img.shields.io/pypi/v/mesa.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/mesa.svg?color=blue&label=Downloads&logo=pypi&logoColor=gold)](https://pypi.org/project/Mesa/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mesa.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/Mesa/) |
-| Meta | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
-| Chat | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Meta    | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) |
+| Chat    | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) |
+| Cite    | [![DOI](https://joss.theoj.org/papers/10.21105/joss.07668/status.svg)](https://doi.org/10.21105/joss.07668) |
 
 Mesa allows users to quickly create agent-based models using built-in
 core components (such as spatial grids and agent schedulers) or
@@ -133,4 +134,7 @@ Don't forget to checkout the [Contributors guide](https://github.com/projectmesa
 
 ## Citing Mesa
 
-To cite Mesa in your publication, you can use the [CITATION.bib](https://github.com/projectmesa/mesa/blob/main/CITATION.bib).
+To cite Mesa in your publication, you can refer to our peer-reviewed article in the Journal of Open Source Software (JOSS):
+- ter Hoeven et al., (2025). Mesa 3: Agent-based modeling with Python in 2025. Journal of Open Source Software, 10(107), 7668, https://doi.org/10.21105/joss.07668
+
+Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) file generates APA, BibTeX and other citation formats.

README.md

@@ -1,5 +1,9 @@
 # Mesa: Agent-based modeling in Python
 
+```{image} https://joss.theoj.org/papers/10.21105/joss.07668/status.svg
+:target: https://doi.org/10.21105/joss.07668
+```
+
 ```{image} https://github.com/projectmesa/mesa/workflows/build/badge.svg
 :target: https://github.com/projectmesa/mesa/actions
 ```
@@ -67,7 +71,14 @@ Mesa is an open source project and welcomes contributions:
 - [Issue Tracker] - Report bugs or suggest features
 - [Contributors Guide] - Learn how to contribute
 
-The original Mesa conference paper is [available here](http://conference.scipy.org.s3-website-us-east-1.amazonaws.com/proceedings/scipy2015/jacqueline_kazil.html).
+### Citing Mesa
+
+To cite Mesa in your publication, you can refer to our peer-reviewed article in the Journal of Open Source Software (JOSS):
+- ter Hoeven et al., (2025). Mesa 3: Agent-based modeling with Python in 2025. Journal of Open Source Software, 10(107), 7668, https://doi.org/10.21105/joss.07668
+
+Our [CITATION.cff](https://github.com/projectmesa/mesa/blob/main/CITATION.cff) file generates APA, BibTeX and other citation formats.
+
+The original Mesa conference paper from 2015 is [available here](http://conference.scipy.org.s3-website-us-east-1.amazonaws.com/proceedings/scipy2015/jacqueline_kazil.html).
 
 ```{toctree}
 :hidden: true